7XX3 | pdb_00007xx3

Crystal structure of human Superoxide Dismutase (SOD1) in complex with a fungal metabolite molecule, Phialomustin B (PB)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.230 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

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This is version 1.2 of the entry. See complete history


Literature

Structural insights into the modulation Of SOD1 aggregation By a fungal metabolite Phialomustin-B: Therapeutic potential in ALS.

Unni, S.Kommu, P.Aouti, S.Nalli, Y.Bharath, M.M.S.Ali, A.Padmanabhan, B.

(2024) PLoS One 19: e0298196-e0298196

  • DOI: https://doi.org/10.1371/journal.pone.0298196
  • Primary Citation of Related Structures:  
    7XX3

  • PubMed Abstract: 

    Amyotrophic lateral sclerosis (ALS) is a fatal human motor neuron disease leading to muscle atrophy and paralysis. Mutations in superoxide dismutase 1 (SOD1) are associated with familial ALS (fALS). The SOD1 mutants in ALS have a toxic-gain of function by destabilizing the functional SOD1 homodimer, consequently inducing fibril-like aggregation with a cytotoxic non-native trimer intermediate. Therefore, reducing SOD1 oligomerization via chemical modulators is an optimal therapy in ALS. Here, we report the discovery of Phialomustin-B, an unsaturated secondary metabolite from the endophytic fungus Phialophora mustea, as a modulator of SOD1 aggregation. The crystal structure of the SOD1-Phialomustin complex refined to 1.90 Å resolution demonstrated for the first time that the ligand binds to the dimer interface and the lateral region near the electrostatic loop. The aggregation analyses of SOD1WT and the disease mutant SOD1A4V revealed that Phialomustin-B reduces cytotoxic trimerization. We propose that Phialomustin-B is a potent lead molecule with therapeutic potential in fALS.


  • Organizational Affiliation
    • Department of Biophysics, National Institute of Mental Health and Neurosciences, Bengaluru, India.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Superoxide dismutase [Cu-Zn]180Homo sapiensMutation(s): 0 
Gene Names: SOD1
EC: 1.15.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00441 (Homo sapiens)
Explore P00441 
Go to UniProtKB:  P00441
PHAROS:  P00441
GTEx:  ENSG00000142168 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00441
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
I2G (Subject of Investigation/LOI)
Query on I2G

Download Ideal Coordinates CCD File 
CA [auth I],
N [auth B],
S [auth D],
V [auth C]
(2~{E},4~{E},6~{S})-4,6-dimethyldeca-2,4-dienoic acid
C12 H20 O2
DZXNZBWYVLLUAX-IVONAZQTSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
L [auth A],
O [auth B],
P [auth B],
Q [auth B],
T [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
X [auth E]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth G]
BA [auth I]
K [auth A]
M [auth B]
R [auth D]
AA [auth G],
BA [auth I],
K [auth A],
M [auth B],
R [auth D],
U [auth C],
W [auth H],
Y [auth E],
Z [auth F]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 242.445α = 90
b = 242.445β = 90
c = 144.491γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Indian Council of Medical ResearchIndiaIndian Council of Medical Research (ICMR),
Department of Science & Technology (DST, India)IndiaDST-FIST: SR/FST/LS-I/2017(C)

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-13
    Type: Initial release
  • Version 1.1: 2024-10-30
    Changes: Structure summary
  • Version 1.2: 2025-02-26
    Changes: Database references